Search Results for "alignment"
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Showing 23 open source projects for "alignment"
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SAM (Sequence Alignment/Map) is a flexible generic format for storing nucleotide sequence alignment. SAMtools provide efficient utilities on manipulating alignments in the SAM format. The main samtools source code repository moved to GitHub in March 2012. For ongoing development since then, see http://github.com/samtools/samtools
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MView
Extract and reformat a sequence database search or multiple alignment
NOTE: The MView repository and web pages have moved to: https://github.com/desmid/mview https://desmid.github.io/mview/ Release tarballs will continue to be uploaded to SourceForge. ---- MView is a command line utility that extracts and reformats the results of a sequence database search or a multiple alignment, optionally adding HTML markup for web page layout. It can also be used as a filter to extract and convert searches or alignments to common formats. Inputs: - Sequence database search: BLAST, FASTA suites. - Multiple sequence alignment: CLUSTAL, HSSP, MSF, FASTA, PIR, MAF. Outputs: - HTML, FASTA, CLUSTAL, MSF, PIR, RDB (tab-separated). ... -
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LF Aligner helps translators create translation memories from texts and their translations. It relies on Hunalign for automatic sentence pairing. Input: txt, doc, docx, rtf, pdf, html. Output: tab delimited txt, TMX and xls. With web features. My email address is listed in readme.txt; for support, use the forum here. My personal website: www.farkastranslations.com.
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TaxOnTree
A program for associating taxonomic information in a phylogenetic tree
TaxOnTree is a phylogenetic program for associating Taxonomic information in a phylogenetic tree. The output is a NEX format tree file configured to be opened in FigTree, that users can promptly color by any taxa or by the ancestrality shared by sequences with query. Input can be a Fasta formatted file to be used in a BLAST search or a list of sequences represented by their identifiers (UniProtAC or NCBI gi), if a cluster is already available. Also, a newick file produced with user software... -
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LMAP_S
Lightweight Multigene Alignment and Phylogeny eStimation
Emanuel Maldonado and Agostinho Antunes (2019) LMAP_S: Lightweight Multigene Alignment and Phylogeny eStimation. BMC Bioinformatics, 20:739. doi: https://doi.org/10.1186/s12859-019-3292-5 -
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MITP
MITP - conserve & novel miRNA identification & target prediction tool
miRNA is a widely known small non-coding RNA which can mediate gene regulation of most important biological processes in plants and animals. Therefore, identification conserve and novel miRNA and their target genes in model and new sequenced species are inevitable. MITP is designed to identify miRNA easily and faster based on sequence mapping result from any mapping software which producing SAM format output result, blast result (default output result) or blat result (default output result).... -
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RGAAT
Reference based genome assembly and annotation for new genome
This program can assemble and/or annotate genome for new genome and known genome upgrade using sequence alignment file (SAM or BAM format), sequence variant file (VCF format or five coloum table (tab-delimited, including chromosome, position, id, reference allele and alternative allele)) or new genome sequence file (FASTA format) based on reference genome sequence file (FASTA format) and annotation file (TBL, GTF, GFF, GFF3 or BED format). -
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SpeedRead
A simple terminal-based open source Spritz-alike
speedread is a terminal-based Spritz-style speed-reading tool that displays text word-by-word to help users read quickly while maintaining comprehension. Inspired by the original Spritz reader, speedread shows one word at a time with alignment to the optimal recognition point (ORP), allowing users to consume content faster than traditional reading methods. -
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Digital Expression on the Web
DEW is a platform that allows users to explore RNA-Seq data
...When provided with multiple isoforms and in the ‘contextual’ mode, corrections include a expectation maximization algorithm estimates effective expression profiles and a corrected alignment is produced. For each gene the user provides, DEW computes coverage descriptive statistics (RPKM, FKMP and total, mean and median corrected counts), expression profiles (normalized as R/FPKM and trimmed mean of fold change). DEW allows users to explore the data by providing interactive graphs. -
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DNATweezer
A suite of BioPerl wrappers for manipulating DNA and protein sequences
...These scripts provide command-line access to the most frequently used BioPerl DNA object methods e.g. reverse-complement and translation of DNA sequences, slicing a sequence alignment, rerooting a phylogenetic tree, and calculating diversity of a population of DNA sequences. -
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FSA is a probabilistic multiple sequence alignment algorithm which uses a "distance-based" approach to aligning homologous protein, RNA or DNA sequences.
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PlaTypUS
Plasmodium Typing Utility Software
The goal of PlaTypUS is to establish a unified Plasmodium whole genome analysis tool, that aligns short read sequences in an agreed upon manner, with many quality control steps, and calls both SNVs and CNVs in a community agreed standard way. We also seek to provide this analysis in a stand-alone graphic user interface so that labs around the world can analyze their own whole genome sequencing data, rather than relying on outside institutes. -
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MspJI-seq_pipeline1.0
an pipeline for MspJI-digesting sequencing in DNA methylation study
...Modification-dependent restriction endonuclease MspJI digestion coupled with next generation sequencing could estimate the methylation state of "CNNR" Cytosine location in the genome by mapping high throughput reads to the reference sequences. MspJI-seq_pipeline1.0 is designed to be a general-purpose mapping program to handle these special characteristics of MspJI-seq. Its alignment is based on the open source program SOAP (Short Oligo Alignment Program), and mCNNR sites recognition is performed by regular expression in perl. -
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Various tools for creating annotated parallel corpora including pre-trained tagging and parsing models for various languages, sentence alignment tools and word alignment tools. Uplug also includes a web-based interface for interactive sentence and word alignment and scripts for indexing and querying parallel corpora using the Corpus Work Bench CWB. Download 'uplug-main' first and then add other packages.
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FFP (Feature frequency profile) is an alignment free comparison tool for phylogenetic analysis and text comparison. It can be applied to nucleotide sequences, complete genomes, proteomes and even used for text comparison.
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MUMmer is a modular system for the rapid whole genome alignment of finished or draft sequence. This package provides an efficient suffix tree library, seed-and-extend alignment, SNP detection, repeat detection, and visualization tools.
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ZORRO is a probabilistic masking program that assigns confidence scores to each column in a multiple seqeunce alignment. These scores can then be used to account for alignment accuracy in phylogenetic inference pipelines.
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Bioinformatics Perl extension for the analysis of antibody variable domain repertoires. Suitable for mammalian repertoire sequences obtained either by Sanger or 454 sequencing. Methods published in Glanville, Zhai, Berka et al, PNAS 2009.
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Whole-genome scale multiple genome local alignment search program. Supports unlimited length gapped-seed patterns, parallelization through distributed hashing, and unique a TF-IDF based repeat filtering method.
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This is a utility to convert a set of fasta formatted sequences along with output from ELAND or SOAP (and other next generation sequence alignment in due time) to make them viewable using eagleview.
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ReAlignerV is an alignment tool focusing on genomic nucleotide sequences upstream of genes. ReAlignerV integrates TRANSFAC(R) Match(TM) results to detect the conserved TFBSs. ReAlignerV is robust against transposable element insertions.
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Scripts to implement Hierarchical Annotation-Dependent Alignment (HADA) protocol for sequence alignment, and related functions.
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IndelExtractor is a GUI and command-line application written in Perl that generates various molecular sequence alignment masks, including one to make identification and removal of Indels and their surrounding ambiguous alignment quick and simple.
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